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Bioinformatics Advance Access originally published online on November 29, 2005
Bioinformatics 2006 22(3):356-358; doi:10.1093/bioinformatics/bti797
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Paircoil2: improved prediction of coiled coils from sequence

A. V. McDonnell 1, T. Jiang 2,{dagger}, A. E. Keating 2,* and B. Berger 1,*

1Mathematics Department, Computer Science and Artificial Intelligence Laboratory Cambridge, MA 02139, USA
2Department of Biology, Massachusetts Institute of Technology Cambridge, MA 02139, USA

*To whom correspondence should be addressed.

Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled–coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.

Availability: Paircoil2 is freely available as a web application and for download at http://paircoil2.csail.mit.edu

Contact: keating{at}mit.edu; bab{at}mit.edu

Supplementary information: Available at Bioinformatics online and at the Paircoil website.

Received on June 26, 2005; revised on November 7, 2005; accepted on November 20, 2005

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